Telomere to telomere genome analysis of Plasmodiophora brassicae

Workflow for the telomere to telomere genome analysis of clubroot pathogen Plasmodiophora brassicae and work published in Genome Biology anf Evolution (GBE) https://doi.org/10.1093/gbe/evae122.

Hybrid Genome Assembly: PacBio Hifi and Oxford Nanopore reads were utilized for hybrid genome assembly using Hifiasm and polished the final assembly with Illumina reads.

Genome Annotations: BRAKER3 pipeline was used that incorporates with GeneMark-ETP + Augustus to train the model with RNASeq and protein evidence to perform the de-novo annotation, followed by TSEBRA mediated integration of both sets to improve accuracy. Link.

Software Installation and Execution: Singularity was used to install/execute the BRAKER3 docker container Link.

1. Detailed T2T genome analysis workflow

2. De novo annotations using BRAKER3 pipeline

3. ChromoMap_R based Ideogram script